A history of halophile research reveals the commitment of scientists to uncovering the secrets of the limits of life, in particular life in high salt concentration and under extreme osmotic pressure. During the last 40 years, halophile scientists have indeed made important contributions to extremophile research, and prior international halophiles congresses have documented both the historical and the current work. During this period of salty discoveries, female scientists, in general, have grown in number worldwide. But those who worked in the field when there were small numbers of women sometimes saw their important contributions overshadowed by their male counterparts. Recent studies suggest that modern female scientists experience gender bias in matters such as conference invitations and even representation among full professors. In the field of halophilic microbiology, what is the impact of gender bias? How has the participation of women changed over time? What do women uniquely contribute to this field? What are factors that impact current female scientists to a greater degree? This essay emphasizes the “her story” (not “history”) of halophile discovery.

As part of their paper they analyze participation of women at conference on halophiles:

This is a useful analysis and compendium and it would be great to see this done for as many fields as possible.

Just found out about this on Facebook via Rod Page: Mesquite V3.0 has been released. Mesquite is from Team Maddison (Wayne and David). I have been using their software since 1987 when I took Stephen Jay Gould's course at Harvard and they were TAs for the course demoing an early version of MacClade. Lots of nice features and it is available in Mac, Unix/Linux, and Windows versions. They describe "What Mesquite Does" on their Wikispaces site in the following way:

Mesquite is software for evolutionary biology, designed to help biologists manage and analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis. Because it is modular, the analyses and management features available depend on the modules installed. Here is a brief overview of some of Mesquite's features. See also a more complete outline of features, and the Mesquite Project Youtube channel, with instructional videos helping you learn Mesquite.

Despite Mesquite's broad analytical capabilities, the developers of Mesquite find that we use Mesquite most often to provide a workflow of data editing, management, and processing. We will therefore begin there.

Just got notified of this by the UC Davis Med. School grants administration: NOT-OD-14-124: NIH Genomic Data Sharing Policy. Lots of interesting things in here including a summary of the comments that they received on the draft policy.

I have copied some of the more interesting and relevant bits below:

Sharing research data supports the NIH mission and is essential to facilitate the translation of research results into knowledge, products, and procedures that improve human health. NIH has longstanding policies to make a broad range of research data, in addition to genomic data, publicly available in a timely manner from the research activities that it funds.

The statement of scope remains intentionally general enough to accommodate the evolving nature of genomic technologies and the broad range of research that generates genomic data.

Several comments were submitted by representatives or members of tribal organizations about data access. Tribal groups expressed concerns about the ability of DACs to represent tribal preferences in the review of requests for tribal data.

The GDS Policy expects that basic sequence and certain related data made available through NIH-designated data repositories and all conclusions derived from them will be freely available. It discourages patenting of “upstream” discoveries, which are considered pre-competitive, while it encourages the patenting of “downstream” applications appropriate for intellectual property.

NIH expects investigators and their institutions to provide basic plans for following this Policy in the “Genomic Data Sharing Plan” located in the Resource Sharing Plan section of funding applications and proposals. Any resources that may be needed to support a proposed genomic data sharing plan (e.g., preparation of data for submission) should be included in the project's budget.

Large-scale non-human genomic data, including data from microbes, microbiomes, and model organisms, as well as relevant associated data (e.g., phenotype and exposure data), are to be shared in a timely manner.

Cutting-edge science has shown that the microbiome is the secret to healthy weight lossand to feeling healthy, energized, optimistic, and at the top of your game. The microbiome is a whole inner world that lives within your intestines—trillions of tiny microbes that help you extract the nutrients from your food, balance your mood, and sharpen your clarity and focus.

These beneficial bacteria make up a separate ecology within the body and have an enormous influence on your metabolism, your hormones, your cravings—even your genes. The microbiome's health is intimately involved with yours: when it flourishes, you flourish. When it craves sugar, so do you. When it operates at peak efficiency, so does your metabolism. And when your microbiome is out of balance, you might find yourself gaining weight or unable to lose weight, no matter how much you exercise or how carefully you eat. To achieve your ideal weight, you need the help of your microbiome.

Now, drawing from nearly two decades of experience as a specialist in functional medicine and intestinal health, Raphael Kellman, MD, has developed the first diet based upon on these scientific breakthroughs. The Microbiome Diet offers an effective three-phase plan to heal your gut, reset your metabolism, and achieve dramatic, sustainable weight loss. The Microbiome Diet will help you...

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With delicious recipes, convenient meal plans, and helpful information on Microbiome Superfoods and Supersupplements—including prebiotics and probiotics—The Microbiome Diet gives you the tools to achieve your healthy weight, boost your mood, regain your mental focus, and be in your best shape for life.

This goes with another YAMMM from Canada recently: Today's YAMMM (Yet Another Mostly Male Meeting) Brought to You by CIFAR & NAS. I have not done any analysis of meetings organized by country but I am thinking it might be worth looking into. I would really suggest if anyone is considering going to this meeting for you to skip it. There should be consequences for such a skewed ratio. And while you are at it consider writing to the organizers and sponsors. I will ...

Friday, August 22, 2014

Well, this is both strange and surreal and fascinating: Who Owns A Monkey's Selfie? No One Can, U.S. Says : The Two-Way : NPR. Turns out the UC Copyright office says a photo taken by a monkey cannot by copyrighted because apparently copyright is reserved for humans (and I guess human corporations). NPR implies that an Ars Technica article by David Kravets is what caught their attention as well as that of others.

I wonder - if one could teach a monkey to type maybe one could get them to type up some papers and then nobody could have copyright on them? What if one wrote a paper where a monkey was a co-author but did not do all the work? Would that mean one could not transfer copyright to anyone else? Seems like I should / could include monkeys on all my work.

Thursday, August 21, 2014

Well, I just got an email invitation to attend CME - OVARIAN CLUB 4. And alas, rather than just dumping it into SPAM (which I did do) I clicked on one of the links. I had to know - what was the gender balance at this meeting. Was there any chance that the organizers would see that it would be ironic to not have a decent number of female speakers? Alas, nope.

The organizing committee is 17:1 males to females.

And the speaker balance is not much better something like 25:6.

I guess maybe they should rename this "Meeting brought to you by people who mostly do not have ovaries." Sad. Another YAMMM (Yet another mostly male meeting).

Wednesday, August 20, 2014

Saw a PR from AAAS about how they were freeing up all of ~ 20 papers on Ebola

In light of what has become the largest Ebola outbreak on record, Science and Science Translational Medicine have compiled over a decade's worth of their published news and research. Researchers and the general public can now view this special collection for free.

OK. More access is good. But alas, they did not even free up all papers in #AAAS journals with Ebola in the Title or Abstract.

And then I started thinking. What about HIV? TB? Malaria?
And as I started Tweeting about this, I saw that ASM also was hopping on the "free Ebola" bandwagon (actually I do not know who did it first).

Yay. All men. How wonderful. Because, you know, there are no women working on the microbiome and nutrition right? Ugg.

Seems like they are still working on getting more speakers. I will send this blog post to the organizers and see what they say. But suffice it to say I am very disappointed in them. Oh, and shockingly, the two organizers are men: Johan Garssen and Alan Landay.

These YAMMMs (Yet Another Mostly Male Meeting) really have got to be killed. People should not got to them. People should not speak at them. And the organizers should not be allowed to run other meetings unless they can explain themselves and provide evidence that they will work to not have this happen again.

UPDATE A FEW MINUTES AFTER POSTING.

I found the program committee for the meeting. Alas the gender ratio there is lame too.

Monday, August 18, 2014

Today, I wanted to show someone a PDF of a paper of mine that I co-authored in 1999. The paper was, I think, kind of cool. It reported the sequencing and analysis of the genome of Deinococcus radiodurans, an incredibly radiation resistant bacterium. Alas, I did not have a copy on me, and the only electornic device I had with me was my phone. The person I wanted to show the paper to had their computer, a device with a strange little red trackball and running some sort of Windows operating system, so I looked at it and panicked and said "Maybe you should drive" (as in, maybe they should be the one controlling the computer).

So this person, who shall remain anonymous mostly because of the ancientness of their computer, did the kind of obvious thing, and opened a web browser (don't even ask which one) and typed in "Pubmed.Com". OK - that would work. I might have preferred going to Google Scholar, but I use Pubmed about as frequently. And though I do not have a Windows machine or the weird web broswser they used, I have recreated what happened next.

A nice Pubmed window. And I said, type in "Deinococcus Eisen." and seven papers showed up.

Anderson said "Although I will not officially assume the role of Science publisher until 3 November, this was too important a task to not carry out immediately. AAAS has always been looking for new ways to reduce the public availability of scientific publications. AAAS approached Snapchat a few months ago and in secret developed a new App "SnapScience" which allows the transient publication of scientific articles. Article longevity can be set to 1 minute, 5 minutes or 15 minutes."

Anderson followed this with "This kind of thing I had always hoped to do in my role as president of the Society for Scholarly Publishing but the technology was just not available. Snapchat has developed the perfect platform for the future of AAAS and scholarly publishing in general with its ability to allow readers a glimpse of a scientific article but not allow them to keep it or reread it or redisplay it."

AAAS CEO Phil Lesher said "We have had serious issues recently with the public demanding access to articles in Science and other AAAS published journals. And in addition, we have published a slew of papers that have needed to be retracted shortly after publication. This solves both issues. First, all papers will only be transiently available, so their there is no need for retractions. Second, even scientists will only have short term access to papers so the public cannot possibly demand access for themselves."

Anderson also said "We think SnapScience is the perfect way for me to step into my new role as Publisher of the Science family of journals. It is cutting edge. It is exactly the type of thing that publishers have been looking for. And it will be fun."

AAAS hopes to roll out updates to SnapScience that will allow researchers to also publish data and protocols only transiently as well.

Well, just got an invite to this meeting: Symbioses becoming permanent: The origins and evolutionary trajectories of organelles. The topic seems of direct interest to what I work on. And, it is relatively close (Irvine is a short hop away). So this could be a way to go to a meeting without having to travel too far. And maybe I could see my younger brother Matt who lives in LA and just graduated from UC Irvine's Masters program in Sound Engineering. Then I looked at the schedule of speakers and organizers. Many are friends. Many others are colleagues. Could be fun to see some people I have not seen in a while. And then I realized, most - no nearly all of them - are men. Below I list the people involved in the meeting, highlighting men in yellow and women in blue.

Eors Szathmary, Loránd University, A fresh look at cooperation in some major transitions, especially the origin of eukaryotes

Marc Ereshefsky, University of Calgary, Evolutionary individuality

Peter Godfrey-Smith, City University of New York, Individuality and the egalitarian transitions

Maureen O’Malley, University of Sydney, Philosophical Reflections on Endosymbiosis: Implications for Evolutionary Theory

Toby Kiers, University Amsterdam, Bacterial cooperativity

Closing remarks J. McCutcheon

So - that appears to be a ratio of 18 male speakers and 4 female speakers for a whopping 18% female speakers. No thanks CIFAR and NAS. I will sign up for a different meeting. And by the way - WTF? There are so so many qualified women working on these topics - what let to this 18:4 ratio? The organizers should really rethink their processes and the sponsors should pull funding from meetings like this. It is the only way some people will pay attention to diversity.

UPDATE: 8/20

Wrote to the NAS via their Website

To whom it may concern:

I am writing to express my disappointment in the gender ratio of speakers at this meeting (18 males, 4 females). Due to the skew I am unwilling to participate. See http://phylogenomics.blogspot.com/2014/08/todays-yammm-yet-another-mostly-male.html for details.

Sincerely,

Jonathan Eisen

Got this response

Dear Dr. Eisen,

The NAS Committee on Scientific Programs, which oversees the Sackler Colloquia most definitely considers gender diversity when approving these programs. When organizers propose the programs they achieve a good balance on paper. Regrettably, in many fields, women scientists are at a premium and are sometimes overwhelmed with invitations and demands for their participation on programs and committees. For a variety of reasons, including availability of speakers, the final program is not always as optimally balanced as originally intended.

I have conveyed your message to NAS Vice President and Chair of the Committee on Scientific Programs and will also share your concerns with the colloquium organizers and co-sponsor.

Thank you very much for the response. It is good to hear there is some emphasis on gender diversity when programs and developed. However, in my experience and based on my readings of the literature on this topic, this is not usually sufficient to produce diverse conferences. Do you know if the NAS has any additional policies relating to diversity at conferences. For example, if someone does not accept an invitation, is the organizer of the meeting then free to select whomever they like or are there protocols to help guarantee that the selection of replacements is also diverse? Also do you know if there are any policies relating to the meetings themselves such as child care that have been shown to impact the attendance of women more than men?

Any additional information you have would be appreciated. I think that NAS could and should do more than just review the proposed list of invitees.

Thursday, August 14, 2014

This is a fascinating read: In Science, It Matters That Women Come Last | FiveThirtyEight. By Emma Pierson, who works at 23 and me. It has all sorts of references of use and details on authorship position in scientific publications and how gender and author position are correlated. Definitely worth a read.

This is a fascinating read: In Science, It Matters That Women Come Last | FiveThirtyEight. By Emma Pierson, who works at 23 and me. It has all sorts of references of use and details on authorship position in scientific publications and how gender and author position are correlated. Definitely worth a read.

Friday, August 01, 2014

Well, been having many discussions recently about PCR amplification happening from "negative" controls where no sample DNA was added. Such amplification is alas pretty common - due to contamination occurring in some other material added to the PCR reaction. Obviously it would be best to eliminate all DNA contamination of all reagents and all PCRs. But if that does not happen, it is possible to try to detect contamination after it has happened. Below I post some papers related to post-sequencing detection of contamination: